Avena sativa, or common oat, is a staple crop and member of the Poaceae or Grass family. Following behind wheat, maize and rice, oats account for 10.5 million hectares of the world’s produced crops as of 2017. Phytocompounds such as β-glucan, avenanthramides, vanillic, syringic, ferric, and caffeic acids have been shown to benefit cardiovascular health or represent prospective benefactors to human health. However, further investigation into these potential benefiting factors requires research that surpasses past works in breadth and scope. Much has been done to bridge the gap in genomic resources for oats, such as the development of high throughput markers, consensus linkage maps and most recently genome sequencing efforts. However, the relative complexity of cultivated oat, an allohexaploid with highly similar subgenomes, provides additional challenges to the development of these resources. A final layer of complexity is the genome size of hexaploid oats, estimated to be approximately 12.8 gigabases, of which a significant portion is composed of complex repetitive elements. Characterization of these highly complex regions is difficult as repetitive regions contained within reads are characteristically difficult to map, thereby complicating assembly efforts and resulting in misassembly and gaps. Through investigation of repetitive elements by creating a novel pipeline capable of offering enhanced resolution, repetitive elements were further examined within well-characterized diploid Avena genomes. To extend on this effort, phylogenetic analyses examining evolutionary relationships between elements in efforts to bolster overall knowledge of the Avena family and the role of transposable elements throughout Avena.